Paraguay is one of the few remaining Latin American countries to still recognise Taiwan after Beijing -- which claims the island as its territory -- spent decades convincing Taipei's diplomatic allies to switch sides.
The foreign ministry said Pena would arrive in Taipei for a five-day trip on Tuesday, and would meet with Taiwanese President Tsai Ing-wen before taking office in August.
"His visit will coincide with the 66th anniversary of the establishment of diplomatic relations between Taiwan and Paraguay on July 12," the ministry said.
"Paraguay is our staunch ally in South America and has firmly supported our participation in the international community for a long time... The ties and friendship between Taiwan and Paraguay are solid."
On the campaign trail, economist and former finance minister Pena had vowed to continue recognising Taiwan, and his win erased Taipei's fear that Paraguay would ditch ties with it in favour of Beijing.
"We are determined to maintain these ties of friendship over the next five years," Pena said in a video message posted on Twitter, adding that he would seek to build "a bilateral agenda... to develop and further strengthen the historic ties between Paraguay and Taiwan".
In recent years, Panama, El Salvador, the Dominican Republic, Nicaragua and Honduras have all switched their diplomatic recognition from Taiwan to China.
Beijing does not permit its own diplomatic allies to also recognise Taipei.
Latin America has been a key diplomatic battleground for China and Taiwan since the end of the Chinese Civil War in 1949.
Honduras became the latest country to switch to Beijing in March, leaving only 13 countries that recognise Taipei.
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